Contacts of the helix formed by residues 218 - 237 (chain B) in PDB entry 4WMJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 218 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B ILE* 3.6 36.8 - - + -
213B SER* 2.8 24.3 + - - -
214B LYS 5.2 0.3 + - - -
215B THR* 3.4 8.9 + - - -
216B PHE 3.8 0.8 - - - -
217B THR* 1.3 69.1 + - - +
219B GLN* 1.3 69.3 + - - +
220B GLU* 3.2 4.7 + - - +
221B THR* 3.2 13.9 + - - +
222B ILE* 2.9 25.9 + - - +
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Residues in contact with GLN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ILE* 3.6 29.7 - - + +
431A ASN* 4.7 4.5 + - - -
217B THR 3.1 7.1 + - - +
218B THR* 1.3 72.1 - - - +
220B GLU* 1.3 72.4 + - - +
222B ILE* 3.9 2.1 - - - +
223B THR* 2.8 41.8 + - - +
525B ALA* 5.9 1.7 - - - +
526B LYS* 5.7 10.1 - - - +
529B GLU* 2.9 38.0 + - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 4.6 3.1 + - - +
391A GLN* 4.7 0.5 + - - -
392A HIS* 2.8 34.9 + - - +
427A ILE* 4.9 5.4 - - + -
431A ASN* 4.6 12.9 + - - +
161B ILE* 3.9 19.8 - - + +
188B SER 4.7 0.7 - - - +
190B ILE* 3.8 43.8 - - + +
218B THR* 4.0 10.4 - - - +
219B GLN* 1.3 91.6 + - + +
221B THR* 1.3 63.4 + - - +
223B THR* 3.3 1.0 + - - -
224B ASN* 3.0 29.9 + - - +
522B LYS* 5.7 3.5 - - - -
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Residues in contact with THR 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 3.6 24.4 - - - +
160B GLY* 3.6 1.9 - - - -
161B ILE* 3.5 29.6 + - - +
211B ILE* 4.1 12.3 - - + -
212B ALA 3.5 23.5 + - - +
213B SER* 4.1 10.1 - - - -
218B THR* 3.2 22.2 + - - +
220B GLU* 1.3 78.0 - - - +
222B ILE* 1.3 58.5 + - + +
224B ASN* 3.4 3.3 + - - +
225B ALA* 2.8 29.8 + - - +
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Residues in contact with ILE 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.4 9.9 - - + -
213B SER* 5.0 1.1 - - - +
216B PHE* 3.5 56.1 - - + +
217B THR* 3.8 11.2 - - - +
218B THR* 2.9 21.6 + - - +
219B GLN* 4.3 2.5 - - - +
221B THR* 1.3 79.2 - - + +
223B THR* 1.3 60.5 + - - +
225B ALA* 3.7 3.3 - - + +
226B THR* 2.8 50.3 + - + +
259B PHE* 5.3 4.7 - - + -
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Residues in contact with THR 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ALA* 5.9 0.4 - - + -
423A ALA* 5.3 6.3 - - + -
424A HIS* 3.6 27.1 - - + +
427A ILE* 3.8 21.2 - - + +
190B ILE* 3.9 17.9 - - + -
219B GLN* 2.8 27.7 + - - +
222B ILE* 1.3 73.2 - - - +
224B ASN* 1.3 65.6 + - - +
226B THR* 3.0 9.7 + - - +
227B SER* 2.9 27.6 + - - +
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Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424A HIS* 3.1 30.3 + - - -
159B ILE* 3.5 25.4 - - + +
187B VAL* 3.8 13.4 - - + +
188B SER* 3.8 7.8 - - - +
189B ASN 3.0 27.9 + - - +
190B ILE* 4.2 1.6 - - - -
191B ASP 5.2 0.2 + - - -
195B LEU* 3.6 24.1 - - + +
220B GLU 3.0 20.1 + - - +
221B THR* 4.9 0.3 - - - -
223B THR* 1.3 75.1 - - - +
225B ALA* 1.3 58.5 + - - +
227B SER 3.3 0.7 + - - -
228B ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.2 10.5 - - + +
211B ILE* 3.6 35.9 - - + -
221B THR 2.8 21.7 + - - +
222B ILE* 3.7 7.4 - - + +
223B THR 3.2 0.4 - - - -
224B ASN* 1.3 75.6 - - - +
226B THR* 1.3 59.5 + - - +
228B ALA* 3.2 3.8 + - - +
229B LYS* 2.9 28.1 + - - +
246B PHE* 4.2 1.2 - - - -
259B PHE* 3.6 18.6 - - + -
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Residues in contact with THR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ILE* 2.8 36.8 + - + +
223B THR* 3.0 18.4 + - - +
225B ALA* 1.3 76.2 - - - +
227B SER* 1.4 58.7 + - - +
229B LYS* 3.3 5.6 + - - +
230B THR* 2.8 35.1 + - - -
259B PHE* 3.8 22.2 - - + -
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Residues in contact with SER 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ILE* 4.5 4.5 - - - -
420A ALA* 3.6 17.2 - - - +
424A HIS* 2.8 32.8 - - - -
195B LEU* 3.6 16.2 - - - -
199B LEU* 4.8 1.7 - - - +
223B THR* 2.9 15.2 + - - +
226B THR* 1.4 75.6 + - - +
228B ALA* 1.3 65.2 + - - +
230B THR* 3.3 8.3 + - - -
231B TRP* 3.0 22.9 + - - +
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B ILE* 4.1 8.5 - - + -
195B LEU* 4.0 10.2 - - + +
199B LEU* 4.7 3.4 - - - -
209B PHE* 3.8 33.9 - - + -
224B ASN 2.9 17.4 + - - +
225B ALA 3.2 5.6 + - - +
227B SER* 1.3 76.3 - - - +
229B LYS* 1.3 57.2 + - - +
231B TRP* 3.3 12.1 + - - +
232B PHE* 3.0 28.1 + - - +
246B PHE* 4.0 6.8 - - + -
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B ALA 2.9 16.4 + - - +
226B THR* 3.5 6.5 - - - +
228B ALA* 1.3 73.9 - - - +
230B THR* 1.3 60.2 + - - +
232B PHE* 3.2 1.8 + - - +
233B LEU* 2.9 56.0 + - + +
242B VAL* 4.7 13.5 - - + -
246B PHE* 3.7 15.4 - - + -
258B ALA 4.8 2.8 + - - -
259B PHE* 2.7 59.5 + - + +
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 2.8 21.3 + - - -
227B SER* 3.3 8.4 + - - -
229B LYS* 1.3 79.3 - - - +
231B TRP* 1.3 63.3 + - - +
233B LEU* 3.9 4.8 - - - +
234B GLU* 3.0 24.2 + - + +
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Residues in contact with TRP 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B LEU* 3.8 57.8 + - + +
202B LEU* 3.6 22.4 - - + -
203B ASN 4.4 0.2 - - - -
204B PRO* 3.5 51.1 - - + +
209B PHE* 3.8 25.6 - + - -
227B SER 3.0 12.2 + - - +
228B ALA 3.4 12.6 - - - +
230B THR* 1.3 76.9 - - - +
232B PHE* 1.3 78.8 + - + +
234B GLU* 3.4 19.9 + - + +
235B ALA* 3.6 6.9 + - - +
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B TYR* 3.8 10.1 - + - -
204B PRO* 3.5 27.6 - - + -
209B PHE* 5.2 3.1 - + - -
228B ALA 3.0 16.3 + - - +
229B LYS 3.5 4.5 - - - +
230B THR 3.2 0.2 - - - -
231B TRP* 1.3 90.0 - + + +
233B LEU* 1.3 68.4 + - + +
235B ALA* 3.0 8.8 + - - +
236B ALA* 2.9 37.1 + - + -
241B ALA* 3.6 31.6 - - + -
242B VAL* 3.9 11.2 - - + -
245B HIS* 3.4 41.3 - + + -
246B PHE* 3.8 21.3 - + + -
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LYS* 2.9 46.2 + - + +
230B THR* 4.1 4.7 - - - +
232B PHE* 1.3 82.9 - - + +
234B GLU* 1.3 67.8 + - - +
235B ALA 3.0 1.8 - - - -
236B ALA 4.0 2.0 - - - +
237B LYS* 2.9 26.5 + - - +
238B ASP 3.5 37.7 - - - +
239B PRO* 4.4 4.7 - - + -
242B VAL* 3.8 17.9 - - + -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B THR* 3.0 15.7 + - + +
231B TRP* 3.5 15.7 - - - +
232B PHE 3.2 0.2 - - - -
233B LEU* 1.3 76.2 - - - +
235B ALA* 1.3 63.3 + - - +
237B LYS* 2.8 35.3 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.7 12.9 + - - +
204B PRO* 3.6 30.5 - - + -
231B TRP 3.6 4.2 + - - +
232B PHE 3.0 8.4 + - - +
233B LEU 3.0 0.4 - - - -
234B GLU* 1.3 88.8 - - - +
236B ALA* 1.3 63.6 + - - +
237B LYS* 3.5 10.0 - - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B TYR* 3.7 26.1 - - + -
232B PHE* 2.9 48.2 + - + +
233B LEU* 4.6 0.7 - - - -
235B ALA* 1.3 73.3 - - - +
237B LYS* 1.3 71.3 + - - +
238B ASP* 3.2 10.7 + - - +
241B ALA* 3.8 13.2 - - + -
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Residues in contact with LYS 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LEU* 2.9 23.6 + - - +
234B GLU* 2.8 35.3 + - - +
235B ALA* 3.9 7.2 - - - +
236B ALA* 1.3 79.7 - - - +
238B ASP* 1.3 57.6 + - - +
239B PRO* 4.5 2.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il